EP3977117A4 - Meso-scale engineered peptides and methods of selecting - Google Patents

Meso-scale engineered peptides and methods of selecting Download PDF

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Publication number
EP3977117A4
EP3977117A4 EP20813167.2A EP20813167A EP3977117A4 EP 3977117 A4 EP3977117 A4 EP 3977117A4 EP 20813167 A EP20813167 A EP 20813167A EP 3977117 A4 EP3977117 A4 EP 3977117A4
Authority
EP
European Patent Office
Prior art keywords
mesoscale
peptides
selection
methods
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
EP20813167.2A
Other languages
German (de)
English (en)
French (fr)
Other versions
EP3977117A1 (en
Inventor
Matthew P. Greving
Kevin Eduard HAUSER
Andrew Morin
Jordan R. WILLIS
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Ibio Inc
Original Assignee
Ibio Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Ibio Inc filed Critical Ibio Inc
Publication of EP3977117A1 publication Critical patent/EP3977117A1/en
Publication of EP3977117A4 publication Critical patent/EP3977117A4/en
Pending legal-status Critical Current

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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/20—Supervised data analysis
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
    • G01N33/6845—Methods of identifying protein-protein interactions in protein mixtures
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K1/00—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length
    • C07K1/10—General methods for the preparation of peptides, i.e. processes for the organic chemical preparation of peptides or proteins of any length using coupling agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/001—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof by chemical synthesis
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00—Machine learning
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00—Machine learning
    • G06N20/20—Ensemble learning
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/045—Combinations of networks
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/0464—Convolutional networks [CNN, ConvNet]
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/0475—Generative networks
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/08—Learning methods
    • G06N3/09—Supervised learning
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N5/00—Computing arrangements using knowledge-based models
    • G06N5/01—Dynamic search techniques; Heuristics; Dynamic trees; Branch-and-bound
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N5/00—Computing arrangements using knowledge-based models
    • G06N5/04—Inference or reasoning models
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B15/00—ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment
    • G16B15/20—Protein or domain folding
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
    • G16B5/30—Dynamic-time models
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00—Machine learning
    • G06N20/10—Machine learning using kernel methods, e.g. support vector machines [SVM]
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/044—Recurrent networks, e.g. Hopfield networks
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

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  • Engineering & Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Molecular Biology (AREA)
  • Software Systems (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Data Mining & Analysis (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • General Physics & Mathematics (AREA)
  • Medical Informatics (AREA)
  • Computing Systems (AREA)
  • Mathematical Physics (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biotechnology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biomedical Technology (AREA)
  • Computational Linguistics (AREA)
  • Organic Chemistry (AREA)
  • Evolutionary Biology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Medicinal Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biochemistry (AREA)
  • Genetics & Genomics (AREA)
  • Immunology (AREA)
  • Hematology (AREA)
  • Urology & Nephrology (AREA)
  • Physiology (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Analytical Chemistry (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Public Health (AREA)
EP20813167.2A 2019-05-31 2020-05-13 Meso-scale engineered peptides and methods of selecting Pending EP3977117A4 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201962855767P 2019-05-31 2019-05-31
PCT/US2020/032715 WO2020242765A1 (en) 2019-05-31 2020-05-13 Meso-scale engineered peptides and methods of selecting

Publications (2)

Publication Number Publication Date
EP3977117A1 EP3977117A1 (en) 2022-04-06
EP3977117A4 true EP3977117A4 (en) 2023-08-16

Family

ID=73553528

Family Applications (2)

Application Number Title Priority Date Filing Date
EP20813167.2A Pending EP3977117A4 (en) 2019-05-31 2020-05-13 Meso-scale engineered peptides and methods of selecting
EP20815607.5A Pending EP3976083A4 (en) 2019-05-31 2020-05-13 MACHINE LEARNING BASED DEVICE FOR THE DEVELOPMENT OF MESO-SCALE PEPTIDES, AND METHOD AND SYSTEM THEREOF

Family Applications After (1)

Application Number Title Priority Date Filing Date
EP20815607.5A Pending EP3976083A4 (en) 2019-05-31 2020-05-13 MACHINE LEARNING BASED DEVICE FOR THE DEVELOPMENT OF MESO-SCALE PEPTIDES, AND METHOD AND SYSTEM THEREOF

Country Status (7)

Country Link
US (3) US11545238B2 (https=)
EP (2) EP3977117A4 (https=)
JP (4) JP7579812B2 (https=)
KR (3) KR20260028069A (https=)
CN (2) CN114585918A (https=)
CA (2) CA3142339A1 (https=)
WO (2) WO2020242765A1 (https=)

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EP3880698A4 (en) 2018-11-14 2022-11-30 RubrYc Therapeutics, Inc. MANIPULATED CD25 POLYPEPTIDES AND USES THEREOF
WO2022243940A1 (en) * 2021-05-21 2022-11-24 Peptone, Ltd. Spacio-temporal determination of polypeptide structure
CN114065620B (zh) * 2021-11-11 2022-06-03 四川大学 基于像素图表征和cnn的可解释性分子动力学轨迹分析方法
US20250299780A1 (en) * 2022-05-06 2025-09-25 Dyno Therapeutics, Inc. System and methods for predicting features of biological sequences
CN115512763B (zh) * 2022-09-06 2023-10-24 北京百度网讯科技有限公司 多肽序列的生成方法、多肽生成模型的训练方法和装置
CN116343922B (zh) * 2022-12-31 2026-01-09 浙江大学杭州国际科创中心 一种基于机器学习对多肽进行预测的方法
CN115881220B (zh) * 2023-02-15 2023-06-06 北京深势科技有限公司 一种抗体结构预测的处理方法和装置
US12587274B2 (en) 2023-03-28 2026-03-24 Quantum Generative Materials Llc Satellite optimization management system based on natural language input and artificial intelligence
CN116467894B (zh) * 2023-05-16 2024-08-20 郑州大学 一种基于机器学习分子动力学的辐照损伤仿真系统及方法
TWI860054B (zh) * 2023-08-22 2024-10-21 國立清華大學 訓練機器學習模型的方法、裝置和電腦程式產品
CN116913395B (zh) * 2023-09-13 2023-11-28 青岛虹竹生物科技有限公司 一种构建小分子肽数据库的数字化方法
WO2025057424A1 (ja) * 2023-09-15 2025-03-20 富士通株式会社 情報処理プログラム，情報処理装置および情報処理方法
US12603701B2 (en) 2023-12-27 2026-04-14 Quantum Generative Materials Llc Distributed satellite constellation management and control system
US12368503B2 (en) 2023-12-27 2025-07-22 Quantum Generative Materials Llc Intent-based satellite transmit management based on preexisting historical location and machine learning

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EP1206494B1 (en) * 1999-08-02 2004-11-03 Synt:Em S.A. Computational design methods for making molecular mimetics
US8374828B1 (en) * 2007-12-24 2013-02-12 The University Of North Carolina At Charlotte Computer implemented system for protein and drug target design utilizing quantified stability and flexibility relationships to control function
US20130090265A1 (en) * 2011-10-11 2013-04-11 Biolauncher Ltd. Systems and methods for generation of context-specific, molecular field-based amino acid substitution matrices
WO2020102603A1 (en) * 2018-11-14 2020-05-22 Rubryc Therapeutics, Inc. Engineered cd25 polypeptides and uses thereof

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EP1206494B1 (en) * 1999-08-02 2004-11-03 Synt:Em S.A. Computational design methods for making molecular mimetics
US8374828B1 (en) * 2007-12-24 2013-02-12 The University Of North Carolina At Charlotte Computer implemented system for protein and drug target design utilizing quantified stability and flexibility relationships to control function
US20130090265A1 (en) * 2011-10-11 2013-04-11 Biolauncher Ltd. Systems and methods for generation of context-specific, molecular field-based amino acid substitution matrices
WO2020102603A1 (en) * 2018-11-14 2020-05-22 Rubryc Therapeutics, Inc. Engineered cd25 polypeptides and uses thereof

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Also Published As

Publication number Publication date
CN114585918A (zh) 2022-06-03
US20230095685A1 (en) 2023-03-30
WO2020242765A1 (en) 2020-12-03
JP2025118804A (ja) 2025-08-13
KR20220039659A (ko) 2022-03-29
CN114401734A (zh) 2022-04-26
JP2022535769A (ja) 2022-08-10
US20210166788A1 (en) 2021-06-03
JP7579812B2 (ja) 2024-11-08
US11545238B2 (en) 2023-01-03
CA3142227A1 (en) 2020-12-03
JP2022535511A (ja) 2022-08-09
KR20220041784A (ko) 2022-04-01
CN114401734B (zh) 2025-06-03
KR20260028069A (ko) 2026-03-03
JP2025016594A (ja) 2025-02-04
EP3976083A4 (en) 2023-07-12
EP3977117A1 (en) 2022-04-06
US20220081472A1 (en) 2022-03-17
CA3142339A1 (en) 2020-12-03
WO2020242766A1 (en) 2020-12-03
EP3976083A1 (en) 2022-04-06

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